I'm not aware of any other reports of this kind of problem and have never seen it myself.
The only thing I can think of that would cause the edit links to not show on other pages is if the user is not in edit roles allowed on the other pages. A user in the admins role should see the links on any page but other users in more specific roles may only see them on the pages where they have edit permissions.
I can't think of any Web.config settings that would affect this, possibly there is some caching issue and touching Web.config clears the cache.
If you really conclude that the change to an older web.config file solves it, then I would recommend inspect both Web.config files very carefully and try to isolate exactly what is different or what specifically solved it.
I recommend always use the Web.config that ships with your version of mojoPortal in general and would be very very surprised if some web.config setting difference is really causing this problem.
If I did encounter this behavior that you describe as a user in the admins role, my first guess would be some strange proxy server configuration might be involved where the web server is not getting the correct host header or cookies passed in the request for some pages.
Hope that helps,
Joe